You have cited two ways to update the interface: Re-running the cosimulation wizard or using the block mask "Ports" tab and using "New" or "Delete" buttons. A third way is the "Autofill" button on that same "Ports" tab.
If the update is small, the "New" / "Delete" method on the Ports tab should be preferred. Adding a new signal or removing an existing one will not affect the remaining current connections to the surrounding model blocks.
There is no way for the tool to know how to connect new ports. If the updates are expected (e.g. a set of debug ports will be added), you can script model updates with commands such as "add_block" and "add_line". See https://www.mathworks.com/help/simulink/programmatic-modeling.html for more infomation.
